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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs28381094

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:48331144 (GRCh38.p14) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.026476 (7008/264690, TOPMED)
A=0.020419 (2865/140310, GnomAD)
A=0.02315 (2222/95970, GnomAD_exome) (+ 15 more)
A=0.00789 (223/28258, 14KJPN)
A=0.01228 (232/18890, ALFA)
A=0.00841 (141/16760, 8.3KJPN)
A=0.0228 (167/7340, ExAC)
A=0.0336 (215/6404, 1000G_30x)
A=0.0313 (157/5008, 1000G)
A=0.0007 (3/4480, Estonian)
A=0.0039 (15/3854, ALSPAC)
A=0.0065 (24/3708, TWINSUK)
A=0.0106 (31/2920, KOREAN)
A=0.0087 (16/1832, Korea1K)
A=0.002 (2/998, GoNL)
A=0.007 (4/600, NorthernSweden)
A=0.093 (20/216, Qatari)
G=0.48 (24/50, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
DUT : 5 Prime UTR Variant
LOC107984755 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 18890 G=0.98772 A=0.01228
European Sub 14286 G=0.99622 A=0.00378
African Sub 2946 G=0.9633 A=0.0367
African Others Sub 114 G=0.956 A=0.044
African American Sub 2832 G=0.9636 A=0.0364
Asian Sub 112 G=1.000 A=0.000
East Asian Sub 86 G=1.00 A=0.00
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 146 G=0.932 A=0.068
Latin American 2 Sub 610 G=0.926 A=0.074
South Asian Sub 98 G=0.98 A=0.02
Other Sub 692 G=0.981 A=0.019


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 G=0.973524 A=0.026476
gnomAD - Genomes Global Study-wide 140310 G=0.979581 A=0.020419
gnomAD - Genomes European Sub 75976 G=0.99643 A=0.00357
gnomAD - Genomes African Sub 42060 G=0.95718 A=0.04282
gnomAD - Genomes American Sub 13668 G=0.94952 A=0.05048
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.9940 A=0.0060
gnomAD - Genomes East Asian Sub 3132 G=0.9933 A=0.0067
gnomAD - Genomes Other Sub 2150 G=0.9712 A=0.0288
gnomAD - Exomes Global Study-wide 95970 G=0.97685 A=0.02315
gnomAD - Exomes European Sub 41390 G=0.99626 A=0.00374
gnomAD - Exomes Asian Sub 25182 G=0.98257 A=0.01743
gnomAD - Exomes American Sub 16366 G=0.91641 A=0.08359
gnomAD - Exomes Ashkenazi Jewish Sub 6234 G=0.9955 A=0.0045
gnomAD - Exomes African Sub 3934 G=0.9522 A=0.0478
gnomAD - Exomes Other Sub 2864 G=0.9846 A=0.0154
14KJPN JAPANESE Study-wide 28258 G=0.99211 A=0.00789
Allele Frequency Aggregator Total Global 18890 G=0.98772 A=0.01228
Allele Frequency Aggregator European Sub 14286 G=0.99622 A=0.00378
Allele Frequency Aggregator African Sub 2946 G=0.9633 A=0.0367
Allele Frequency Aggregator Other Sub 692 G=0.981 A=0.019
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.926 A=0.074
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.932 A=0.068
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=0.98 A=0.02
8.3KJPN JAPANESE Study-wide 16760 G=0.99159 A=0.00841
ExAC Global Study-wide 7340 G=0.9772 A=0.0228
ExAC Asian Sub 5278 G=0.9735 A=0.0265
ExAC Europe Sub 1754 G=0.9937 A=0.0063
ExAC African Sub 152 G=0.934 A=0.066
ExAC Other Sub 90 G=0.96 A=0.04
ExAC American Sub 66 G=0.97 A=0.03
1000Genomes_30x Global Study-wide 6404 G=0.9664 A=0.0336
1000Genomes_30x African Sub 1786 G=0.9468 A=0.0532
1000Genomes_30x Europe Sub 1266 G=0.9953 A=0.0047
1000Genomes_30x South Asian Sub 1202 G=0.9676 A=0.0324
1000Genomes_30x East Asian Sub 1170 G=0.9957 A=0.0043
1000Genomes_30x American Sub 980 G=0.929 A=0.071
1000Genomes Global Study-wide 5008 G=0.9687 A=0.0313
1000Genomes African Sub 1322 G=0.9523 A=0.0477
1000Genomes East Asian Sub 1008 G=0.9960 A=0.0040
1000Genomes Europe Sub 1006 G=0.9950 A=0.0050
1000Genomes South Asian Sub 978 G=0.965 A=0.035
1000Genomes American Sub 694 G=0.927 A=0.073
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9993 A=0.0007
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9961 A=0.0039
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9935 A=0.0065
KOREAN population from KRGDB KOREAN Study-wide 2920 G=0.9894 A=0.0106
Korean Genome Project KOREAN Study-wide 1832 G=0.9913 A=0.0087
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.998 A=0.002
Northern Sweden ACPOP Study-wide 600 G=0.993 A=0.007
Qatari Global Study-wide 216 G=0.907 A=0.093
SGDP_PRJ Global Study-wide 50 G=0.48 A=0.52
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p14 chr 15 NC_000015.10:g.48331144G>A
GRCh37.p13 chr 15 NC_000015.9:g.48623341G>A
DUT RefSeqGene NG_029497.1:g.4721G>A
Gene: DUT, deoxyuridine triphosphatase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
DUT transcript variant 4 NM_001330286.2:c.-23= N/A 5 Prime UTR Variant
DUT transcript variant 1 NM_001025248.2:c. N/A Genic Upstream Transcript Variant
DUT transcript variant 3 NM_001025249.1:c. N/A Genic Upstream Transcript Variant
DUT transcript variant 2 NM_001948.4:c. N/A Genic Upstream Transcript Variant
Gene: LOC107984755, uncharacterized LOC107984755 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC107984755 transcript variant X1 XR_007064623.1:n. N/A Intron Variant
LOC107984755 transcript variant X2 XR_007064624.1:n. N/A Genic Upstream Transcript Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement G= A
GRCh38.p14 chr 15 NC_000015.10:g.48331144= NC_000015.10:g.48331144G>A
GRCh37.p13 chr 15 NC_000015.9:g.48623341= NC_000015.9:g.48623341G>A
DUT RefSeqGene NG_029497.1:g.4721= NG_029497.1:g.4721G>A
DUT transcript variant 4 NM_001330286.2:c.-23= NM_001330286.2:c.-23G>A
DUT transcript variant 4 NM_001330286.1:c.-23= NM_001330286.1:c.-23G>A
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

46 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 EGP_SNPS ss35072743 May 24, 2005 (125)
2 1000GENOMES ss211605537 Jul 14, 2010 (132)
3 1000GENOMES ss338762417 May 09, 2011 (134)
4 TISHKOFF ss564466220 Apr 25, 2013 (138)
5 SSMP ss660186284 Apr 25, 2013 (138)
6 EVA-GONL ss991760502 Aug 21, 2014 (142)
7 1000GENOMES ss1353363713 Aug 21, 2014 (142)
8 EVA_UK10K_ALSPAC ss1632943092 Apr 01, 2015 (144)
9 EVA_UK10K_TWINSUK ss1675937125 Apr 01, 2015 (144)
10 EVA_EXAC ss1691818391 Apr 01, 2015 (144)
11 EVA_DECODE ss1695776663 Apr 01, 2015 (144)
12 HAMMER_LAB ss1808192333 Sep 08, 2015 (146)
13 WEILL_CORNELL_DGM ss1935164452 Feb 12, 2016 (147)
14 GENOMED ss1968100111 Jul 19, 2016 (147)
15 HUMAN_LONGEVITY ss2206567542 Dec 20, 2016 (150)
16 GRF ss2701231171 Nov 08, 2017 (151)
17 GNOMAD ss2741229738 Nov 08, 2017 (151)
18 GNOMAD ss2749300399 Nov 08, 2017 (151)
19 GNOMAD ss2934616357 Nov 08, 2017 (151)
20 EGCUT_WGS ss3680382353 Jul 13, 2019 (153)
21 EVA_DECODE ss3697843184 Jul 13, 2019 (153)
22 ACPOP ss3740901256 Jul 13, 2019 (153)
23 EVA ss3753053339 Jul 13, 2019 (153)
24 KHV_HUMAN_GENOMES ss3818371874 Jul 13, 2019 (153)
25 EVA ss3834221624 Apr 27, 2020 (154)
26 SGDP_PRJ ss3882864765 Apr 27, 2020 (154)
27 KRGDB ss3932023450 Apr 27, 2020 (154)
28 KOGIC ss3976090661 Apr 27, 2020 (154)
29 FSA-LAB ss3984072728 Apr 27, 2021 (155)
30 EVA ss3986647545 Apr 27, 2021 (155)
31 TOPMED ss4990493535 Apr 27, 2021 (155)
32 TOMMO_GENOMICS ss5216076930 Apr 27, 2021 (155)
33 1000G_HIGH_COVERAGE ss5298354742 Oct 16, 2022 (156)
34 EVA ss5419078526 Oct 16, 2022 (156)
35 HUGCELL_USP ss5492092810 Oct 16, 2022 (156)
36 EVA ss5511420468 Oct 16, 2022 (156)
37 1000G_HIGH_COVERAGE ss5599714910 Oct 16, 2022 (156)
38 EVA ss5623964281 Oct 16, 2022 (156)
39 SANFORD_IMAGENETICS ss5657460457 Oct 16, 2022 (156)
40 TOMMO_GENOMICS ss5769849851 Oct 16, 2022 (156)
41 EVA ss5800068068 Oct 16, 2022 (156)
42 YY_MCH ss5815310967 Oct 16, 2022 (156)
43 EVA ss5828168221 Oct 16, 2022 (156)
44 EVA ss5851282315 Oct 16, 2022 (156)
45 EVA ss5875775552 Oct 16, 2022 (156)
46 EVA ss5948858777 Oct 16, 2022 (156)
47 1000Genomes NC_000015.9 - 48623341 Oct 12, 2018 (152)
48 1000Genomes_30x NC_000015.10 - 48331144 Oct 16, 2022 (156)
49 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 48623341 Oct 12, 2018 (152)
50 Genetic variation in the Estonian population NC_000015.9 - 48623341 Oct 12, 2018 (152)
51 ExAC NC_000015.9 - 48623341 Oct 12, 2018 (152)
52 gnomAD - Genomes NC_000015.10 - 48331144 Apr 27, 2021 (155)
53 gnomAD - Exomes NC_000015.9 - 48623341 Jul 13, 2019 (153)
54 Genome of the Netherlands Release 5 NC_000015.9 - 48623341 Apr 27, 2020 (154)
55 KOREAN population from KRGDB NC_000015.9 - 48623341 Apr 27, 2020 (154)
56 Korean Genome Project NC_000015.10 - 48331144 Apr 27, 2020 (154)
57 Northern Sweden NC_000015.9 - 48623341 Jul 13, 2019 (153)
58 Qatari NC_000015.9 - 48623341 Apr 27, 2020 (154)
59 SGDP_PRJ NC_000015.9 - 48623341 Apr 27, 2020 (154)
60 8.3KJPN NC_000015.9 - 48623341 Apr 27, 2021 (155)
61 14KJPN NC_000015.10 - 48331144 Oct 16, 2022 (156)
62 TopMed NC_000015.10 - 48331144 Apr 27, 2021 (155)
63 UK 10K study - Twins NC_000015.9 - 48623341 Oct 12, 2018 (152)
64 ALFA NC_000015.10 - 48331144 Apr 27, 2021 (155)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss211605537, ss1695776663 NC_000015.8:46410632:G:A NC_000015.10:48331143:G:A (self)
66431954, 36876167, 26120601, 2191227, 10494894, 16469632, 39200844, 14186121, 17206382, 34881745, 74046237, 36876167, ss338762417, ss564466220, ss660186284, ss991760502, ss1353363713, ss1632943092, ss1675937125, ss1691818391, ss1808192333, ss1935164452, ss1968100111, ss2701231171, ss2741229738, ss2749300399, ss2934616357, ss3680382353, ss3740901256, ss3753053339, ss3834221624, ss3882864765, ss3932023450, ss3984072728, ss3986647545, ss5216076930, ss5419078526, ss5511420468, ss5623964281, ss5657460457, ss5800068068, ss5828168221, ss5948858777 NC_000015.9:48623340:G:A NC_000015.10:48331143:G:A (self)
87240845, 468331936, 32468662, 103686955, 206039195, 8375177339, ss2206567542, ss3697843184, ss3818371874, ss3976090661, ss4990493535, ss5298354742, ss5492092810, ss5599714910, ss5769849851, ss5815310967, ss5851282315, ss5875775552 NC_000015.10:48331143:G:A NC_000015.10:48331143:G:A (self)
ss35072743 NT_010194.17:19413897:G:A NC_000015.10:48331143:G:A (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs28381094

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top▲ Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post761+d5e8e07